I am having difficulty w/ this option, so I decided to start a brand new project from scratch to see if I could get it to work/fail.

1) I started a new VS2010 (C#) WPF project, called it SmartAssemblyTesting
2) I built this project in Release mode
3) I started a new SmartAssembly project, pointing the source to my .exe to the Release folder of my VS project.
4) I then pointed the destination to a different folder.
5) Now the only option I activated in S/A is the Strong Name Signing. I point it to a .PFX file, and enter the password.
6) All good so far, so I hit Build
7) I ran the .exe in the destination folder. Fail.
8 ) I rebuilt the S/A project w/ Self-Diagnostics
9) I re-ran the .exe in the destination folder. Fail.

It shows this message:
System.IO.FileLoadException: Could not load file or assembly 'SmartAssemblyTesting, PublicKeyToken=null' or one of its dependencies. The located assembly's manifest definition does not match the assembly reference. (Exception from HRESULT: 0x80131040)

There are no external dependencies (that are not defined in the GAC) for this project.

Well, I have an update. I started a brand new project (again) for more experimenting. This time however, I checked the project property Signing >> [X] Sign the assembly, and pointed it to the PFX file.

This time the project worked. Uncheck the option and it breaks again.

Seems S/A should warn against this situation, but at least I have something to focus on now on my "real" project.